I like some of the ship retrofit ideas I've seen. Particularly the option to unlock a retrofit for a favorite ship (or a few favorites) at Tier5.
Personally though I find simply bumping up a retrofit to tier5 specs somewhat unimaginative. Instead what if a retrofit would raise the ship stats a little (additional console or two, additional BO slot or two, some additional hull and shield) but also unlock one special ability. This special ability would be based on the ship class and tier being unlocked and be something that any group would love to have along in an end game group.
T2 escort retrofit = +some shields & hull, +1 eng, tac, sci console each, +1 eng, tac, sci BO slot each. unlock special ability "tenacity": 3km Allied link (similar in execution to extend shields) that gives +some dps and greatly boosts evasion for it's duration.
T2 sci vessel = +some shields & hull, +1 eng, tac, sci console each, +1 eng, tac, sci BO slot each. unlock special ability "scan bouy": Drop a small stationary scan bouy with a 100km(?) range. Everything in range of the bouy's radius shows up on the mini-map and big area map, cloaked vessels included however they would not be targetable unless detected through normal means.
Just which ship classes and tiers should get what kind of special ability are of course subject to debate. However I'm just trying to think of ways to make the lower tier ships desireable to have in the end game without simply making them reskinned tier5's.